# WELCOME TO RadaR

#RadaR is licensed under the GNU General Public License (GPL) v2.0 (https://github.com/ceefluz/radar/blob/master/LICENSE)

# LIST OF REQUIRED PACKAGES -----------------------------------------------
library(shiny)
library(shinydashboard)
library(shinydashboardPlus)
library(dashboardthemes)
library(shinyWidgets)
library(shinycssloaders)
library(shinyjs)
library(DT)
library(tidyverse)
library(ggtext)
library(AMR)
library(cleaner)
library(scales)
library(ggiraph)

source('interfaces.R')

trsns <- read_tsv("translations.txt", lazy = FALSE)
# to do: make system settings dependent
trnslt <- function(english, new_lang = "nl", file = trsns) {
  if (english %in% trsns[, 1, drop = TRUE]) {
    trsns[match(english, trsns[, 1, drop = TRUE]), new_lang, drop = TRUE]
  } else {
    english
  }
}

pathogens <- read_csv("data/grouping microorganisms.csv")

# created by calling createAbMapping()
tAntibiotics = readxl::read_xlsx('data/ab_mapping.xlsx') %>% 
  select(Mnemonic, Naam, `EARS-Net.Mnemonic`, `EARS-Net.Name`)

# radar_data <- readGlimsArchive(ymdStartDate = ymdStartDate,
#                                ymdEndDate = ymdEndDate, 
#                                readPreprocessed = T)
radar_data <- readGlimsFinalResults() %>% 
  mutate_if(is.rsi, as.sir)

if (!'CRO' %in% colnames(radar_data))
  radar_data <- radar_data %>% add_column('CRO' = '')

if (!'OXA' %in% colnames(radar_data))
  radar_data <- radar_data %>% add_column('OXA' = '')

specialties <- read_csv("data/specialties.csv", lazy = FALSE)

specialties <- specialties %>%
  mutate(specialty_shiny = if_else(specialty != "Outpatients", paste0(specialty, " (", str_replace_all(specialism, ";", ", "), ")"), "Outpatients"),
         department = if_else(is.na(department), "NO DEPARTMENT GIVEN", department))

specialties <- separate_rows(specialties, specialism, sep = ";")

specialties <- separate_rows(specialties, department, sep = ";")


radar_data <- radar_data %>% 
  left_join(specialties) %>% 
  mutate(specialty = if_else(is.na(specialty), "NO SPECIALTY GIVEN", specialty),
         specialty_shiny = if_else(is.na(specialty_shiny), "NO SPECIALTY GIVEN", specialty_shiny),
         name = mo_name(mo),
         FLC = OXA) %>% 
  left_join(pathogens) 

lab_ab <- c("CFCC", "CFCL", "CFOC", "CFSC", "CFTC", "COCL", "GEHI", "QUDA")

radar_data <- radar_data %>%
  select_at(vars(!contains(lab_ab))) %>%
  rename_if(is.rsi, function(x) ifelse(is.na(suppressWarnings(as.ab(x))),
                                       x,
                                       suppressWarnings(as.ab(x)))) %>% 
  mutate(group_all = 1) # dummy variable to disable grouping

radar_data <- radar_data %>% 
  mutate(CRO = if_else(is.na(CRO) & !is.na(CTX), CTX, CRO))

suppressMessages(
  radar_data_first <- radar_data %>% 
    filter_first_isolate(col_patient_id = "patientid", episode_days = 365, info = FALSE) %>% 
    mutate(mo = as.mo(mo, Becker = TRUE))
)

intrinsic_info <- AMR::intrinsic_resistant %>% 
  mutate(#mo = as.mo(microorganism), 
         intrinsic_r = TRUE)


download_box <- function(exportname, plot) {
  downloadHandler(
    filename = function() {
      paste(exportname, Sys.Date(), ".png", sep = "")
    },
    content = function(file) {
      ggsave(file, plot = plot, device = "png", width = 8)
    }
  )
}